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        <a href="dadi-module.html">Package&nbsp;dadi</a> ::
        Module&nbsp;Misc
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<h1 class="epydoc">Source Code for <a href="dadi.Misc-module.html">Module dadi.Misc</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">Miscellaneous utility functions. Including ms simulation.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt><tt class="py-name">sys</tt><tt class="py-op">,</tt><tt class="py-name">time</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">linalg</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"># Nucleotide order assumed in Q matrices.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable dadi.Misc.code=dadi.Misc-module.html#code"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-0', 'code', 'link-0');">code</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'CGTA'</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-comment">#: Storage for times at which each stream was flushed.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable dadi.Misc.__times_last_flushed=dadi.Misc-module.html#__times_last_flushed"><a title="dadi.Misc.__times_last_flushed" class="py-name" href="#" onclick="return doclink('link-1', '__times_last_flushed', 'link-1');">__times_last_flushed</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="delayed_flush"></a><div id="delayed_flush-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="delayed_flush-toggle" onclick="return toggle('delayed_flush');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#delayed_flush">delayed_flush</a><tt class="py-op">(</tt><tt class="py-param">stream</tt><tt class="py-op">=</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdout</tt><tt class="py-op">,</tt> <tt class="py-param">delay</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="delayed_flush-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="delayed_flush-expanded"><a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">    Flush a stream, ensuring that it is only flushed every 'delay' *minutes*.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring">    Note that upon the first call to this method, the stream is not flushed.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">    stream: The stream to flush. For this to work with simple 'print'</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring">            statements, the stream should be sys.stdout.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">    delay: Minimum time *in minutes* between flushes.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">    This function is useful to prevent I/O overload on the cluster.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">    <tt class="py-keyword">global</tt> <tt id="link-2" class="py-name"><a title="dadi.Misc.__times_last_flushed" class="py-name" href="#" onclick="return doclink('link-2', '__times_last_flushed', 'link-1');">__times_last_flushed</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-name">curr_time</tt> <tt class="py-op">=</tt> <tt class="py-name">time</tt><tt class="py-op">.</tt><tt class="py-name">time</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-comment"># If this is the first time this method has been called with this stream,</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-comment"># we need to fill in the times_last_flushed dict. setdefault will do this</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">    <tt class="py-comment"># without overwriting any entry that may be there already.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">stream</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-3" class="py-name"><a title="dadi.Misc.__times_last_flushed" class="py-name" href="#" onclick="return doclink('link-3', '__times_last_flushed', 'link-1');">__times_last_flushed</a></tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt id="link-4" class="py-name"><a title="dadi.Misc.__times_last_flushed" class="py-name" href="#" onclick="return doclink('link-4', '__times_last_flushed', 'link-1');">__times_last_flushed</a></tt><tt class="py-op">[</tt><tt class="py-name">stream</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">curr_time</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-name">last_flushed</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="dadi.Misc.__times_last_flushed" class="py-name" href="#" onclick="return doclink('link-5', '__times_last_flushed', 'link-1');">__times_last_flushed</a></tt><tt class="py-op">[</tt><tt class="py-name">stream</tt><tt class="py-op">]</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">    <tt class="py-comment"># Note that time.time() returns values in seconds, hence the factor of 60.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">curr_time</tt> <tt class="py-op">-</tt> <tt class="py-name">last_flushed</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">delay</tt><tt class="py-op">*</tt><tt class="py-number">60</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt class="py-name">flush</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">        <tt id="link-6" class="py-name"><a title="dadi.Misc.__times_last_flushed" class="py-name" href="#" onclick="return doclink('link-6', '__times_last_flushed', 'link-1');">__times_last_flushed</a></tt><tt class="py-op">[</tt><tt class="py-name">stream</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">curr_time</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"> </tt>
<a name="ensure_1arg_func"></a><div id="ensure_1arg_func-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="ensure_1arg_func-toggle" onclick="return toggle('ensure_1arg_func');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#ensure_1arg_func">ensure_1arg_func</a><tt class="py-op">(</tt><tt class="py-param">var</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ensure_1arg_func-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ensure_1arg_func-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">    Ensure that var is actually a one-argument function.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">    This is primarily used to convert arguments that are constants into</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">    trivial functions of time for use in integrations where parameters are</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    allowed to change over time.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">isscalar</tt><tt class="py-op">(</tt><tt class="py-name">var</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-comment"># If a constant was passed in, use lambda to make it a nice</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">        <tt class="py-comment">#  simple function.</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt class="py-name">var_f</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">var</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">        <tt class="py-name">var_f</tt> <tt class="py-op">=</tt> <tt class="py-name">var</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">callable</tt><tt class="py-op">(</tt><tt class="py-name">var_f</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Argument is not a constant or a function.'</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">        <tt class="py-name">var_f</tt><tt class="py-op">(</tt><tt class="py-number">0.0</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt class="py-name">TypeError</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Argument is not a constant or a one-argument '</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">                         <tt class="py-string">'function.'</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">var_f</tt> </tt>
</div><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="ms_command"></a><div id="ms_command-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="ms_command-toggle" onclick="return toggle('ms_command');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#ms_command">ms_command</a><tt class="py-op">(</tt><tt class="py-param">theta</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">core</tt><tt class="py-op">,</tt> <tt class="py-param">iter</tt><tt class="py-op">,</tt> <tt class="py-param">recomb</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">rsites</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ms_command-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ms_command-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">    Generate ms command for simulation from core.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">    theta: Assumed theta</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">    ns: Sample sizes</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">    core: Core of ms command that specifies demography.</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">    iter: Iterations to run ms</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">    recomb: Assumed recombination rate</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    rsites: Sites for recombination. If None, default is 10*theta.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">        <tt id="link-7" class="py-name" targets="Function dadi.Misc.ms_command()=dadi.Misc-module.html#ms_command"><a title="dadi.Misc.ms_command" class="py-name" href="#" onclick="return doclink('link-7', 'ms_command', 'link-7');">ms_command</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ms %(total_chrom)i %(iter)i -t %(theta)f -I %(numpops)i "</tt>\ </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">                <tt class="py-string">"%(sample_sizes)s %(core)s"</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt id="link-8" class="py-name"><a title="dadi.Misc.ms_command" class="py-name" href="#" onclick="return doclink('link-8', 'ms_command', 'link-7');">ms_command</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"ms %(total_chrom)i %(iter)i -t %(theta)f  %(core)s"</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">recomb</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt id="link-9" class="py-name"><a title="dadi.Misc.ms_command" class="py-name" href="#" onclick="return doclink('link-9', 'ms_command', 'link-7');">ms_command</a></tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="dadi.Misc.ms_command" class="py-name" href="#" onclick="return doclink('link-10', 'ms_command', 'link-7');">ms_command</a></tt> <tt class="py-op">+</tt> <tt class="py-string">" -r %(recomb)f %(rsites)i"</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">rsites</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">            <tt class="py-name">rsites</tt> <tt class="py-op">=</tt> <tt class="py-name">theta</tt><tt class="py-op">*</tt><tt class="py-number">10</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-name">sub_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'total_chrom'</tt><tt class="py-op">:</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'iter'</tt><tt class="py-op">:</tt> <tt class="py-name">iter</tt><tt class="py-op">,</tt> <tt class="py-string">'theta'</tt><tt class="py-op">:</tt> <tt class="py-name">theta</tt><tt class="py-op">,</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">                <tt class="py-string">'numpops'</tt><tt class="py-op">:</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'sample_sizes'</tt><tt class="py-op">:</tt> <tt class="py-string">' '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">                <tt class="py-string">'core'</tt><tt class="py-op">:</tt> <tt class="py-name">core</tt><tt class="py-op">,</tt> <tt class="py-string">'recomb'</tt><tt class="py-op">:</tt> <tt class="py-name">recomb</tt><tt class="py-op">,</tt> <tt class="py-string">'rsites'</tt><tt class="py-op">:</tt> <tt class="py-name">rsites</tt><tt class="py-op">}</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-11" class="py-name"><a title="dadi.Misc.ms_command" class="py-name" href="#" onclick="return doclink('link-11', 'ms_command', 'link-7');">ms_command</a></tt> <tt class="py-op">%</tt> <tt class="py-name">sub_dict</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"> </tt>
<a name="perturb_params"></a><div id="perturb_params-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="perturb_params-toggle" onclick="return toggle('perturb_params');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#perturb_params">perturb_params</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">fold</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">lower_bound</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">upper_bound</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="perturb_params-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="perturb_params-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring">    Generate a perturbed set of parameters.</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">    Each element of params is radomly perturbed &lt;fold&gt; factors of 2 up or down.</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-docstring">    fold: Number of factors of 2 to perturb by</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring">    lower_bound: If not None, the resulting parameter set is adjusted to have </tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">                 all value greater than lower_bound.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">    upper_bound: If not None, the resulting parameter set is adjusted to have </tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt class="py-docstring">                 all value less than upper_bound.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-name">pnew</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt id="link-12" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.fold()=dadi.Spectrum_mod.Spectrum-class.html#fold"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-12', 'fold', 'link-12');">fold</a></tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">params</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">lower_bound</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">bound</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">lower_bound</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">bound</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">                <tt class="py-name">lower_bound</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">        <tt class="py-name">pnew</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">pnew</tt><tt class="py-op">,</tt> <tt class="py-number">1.01</tt><tt class="py-op">*</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">lower_bound</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">upper_bound</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">bound</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">upper_bound</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">bound</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">                <tt class="py-name">upper_bound</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">inf</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-name">pnew</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">pnew</tt><tt class="py-op">,</tt> <tt class="py-number">0.99</tt><tt class="py-op">*</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">upper_bound</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">pnew</tt> </tt>
</div><a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"> </tt>
<a name="make_fux_table"></a><div id="make_fux_table-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="make_fux_table-toggle" onclick="return toggle('make_fux_table');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#make_fux_table">make_fux_table</a><tt class="py-op">(</tt><tt class="py-param">fid</tt><tt class="py-op">,</tt> <tt class="py-param">ts</tt><tt class="py-op">,</tt> <tt class="py-param">Q</tt><tt class="py-op">,</tt> <tt class="py-param">tri_freq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="make_fux_table-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_fux_table-expanded"><a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"><tt class="py-docstring">    Make file of 1-fux for use in ancestral misidentification correction.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"><tt class="py-docstring">    fid: Filename to output to.</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"><tt class="py-docstring">    ts: Expected number of substitutions per site between ingroup and outgroup.</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-docstring">    Q: Trinucleotide transition rate matrix. This should be a 64x64 matrix, in</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"><tt class="py-docstring">       which entries are ordered using the code CGTA -&gt; 0,1,2,3. For example, </tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-docstring">       ACT -&gt; 3*16+0*4+2*1=50. The transition rate from ACT to AGT is then </tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-docstring">       entry 50,54.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-docstring">    tri_freq: Dictionary in which each entry maps a trinucleotide to its </tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-docstring">              ancestral frequency. e.g. {'AAA': 0.01, 'AAC':0.012...}</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-docstring">              Note that should be the frequency in the entire region scanned</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"><tt class="py-docstring">              for variation, not just sites where there are SNPs.</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-comment"># Ensure that the *columns* of Q sum to zero.</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">    <tt class="py-comment"># That is the correct condition when Q_{i,j} is the rate from i to j.</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">    <tt class="py-comment"># This indicates a typo in Hernandez, Williamson, and Bustamante.</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">Q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">        <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">Q</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">Q</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-name">Q</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-name">s</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">    <tt class="py-name">eQhalf</tt> <tt class="py-op">=</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">linalg</tt><tt class="py-op">.</tt><tt class="py-name">matfuncs</tt><tt class="py-op">.</tt><tt class="py-name">expm</tt><tt class="py-op">(</tt><tt class="py-name">Q</tt> <tt class="py-op">*</tt> <tt class="py-name">ts</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'write'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt class="py-name">fid</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    <tt class="py-name">outlines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">first_ii</tt><tt class="py-op">,</tt><tt class="py-name">first</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-13', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">x_ii</tt><tt class="py-op">,</tt><tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-14', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">third_ii</tt><tt class="py-op">,</tt><tt class="py-name">third</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-15', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">                <tt class="py-comment"># This the index into Q and eQ</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">                <tt class="py-name">xind</tt> <tt class="py-op">=</tt> <tt class="py-number">16</tt><tt class="py-op">*</tt><tt class="py-name">first_ii</tt><tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">*</tt><tt class="py-name">x_ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">*</tt><tt class="py-name">third_ii</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">u_ii</tt><tt class="py-op">,</tt><tt class="py-name">u</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-16', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">                    <tt class="py-comment"># This the index into Q and eQ</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">                    <tt class="py-name">uind</tt> <tt class="py-op">=</tt> <tt class="py-number">16</tt><tt class="py-op">*</tt><tt class="py-name">first_ii</tt><tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">*</tt><tt class="py-name">u_ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">*</tt><tt class="py-name">third_ii</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">                    <tt class="py-comment">## Note that the Q terms factor out in our final</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">                    <tt class="py-comment">## calculation, because for both PMuUu and PMuUx the final</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">                    <tt class="py-comment">## factor in Eqn 2 is P(S={u,x}|M=u).</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">                    <tt class="py-comment">#Qux = Q[uind,xind]</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">                    <tt class="py-comment">#denomu = Q[uind].sum() - Q[uind,uind]</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">                    <tt class="py-name">PMuUu</tt><tt class="py-op">,</tt> <tt class="py-name">PMuUx</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">                    <tt class="py-comment"># Equation 2 in HWB. We have to generalize slightly to</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">                    <tt class="py-comment"># calculate PMuUx. In calculate PMuUx, we're summing over</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">                    <tt class="py-comment"># alpha the probability that the MRCA was alpha, and it</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">                    <tt class="py-comment"># substituted to x on the outgroup branch, and it</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">                    <tt class="py-comment"># substituted to u on the ingroup branch, and it mutated to</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">                    <tt class="py-comment"># x in the ingroup (conditional on it having mutated in the</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">                    <tt class="py-comment"># ingroup). Note that the mutation to x condition cancels</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">                    <tt class="py-comment"># in fux, so we don't bother to calculate it.</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">                    <tt class="py-keyword">for</tt> <tt class="py-name">aa</tt><tt class="py-op">,</tt><tt class="py-name">alpha</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-17', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">                        <tt class="py-name">aind</tt> <tt class="py-op">=</tt> <tt class="py-number">16</tt><tt class="py-op">*</tt><tt class="py-name">first_ii</tt><tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">*</tt><tt class="py-name">aa</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">*</tt><tt class="py-name">third_ii</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">                        <tt class="py-name">pia</tt> <tt class="py-op">=</tt> <tt class="py-name">tri_freq</tt><tt class="py-op">[</tt><tt class="py-name">first</tt><tt class="py-op">+</tt><tt class="py-name">alpha</tt><tt class="py-op">+</tt><tt class="py-name">third</tt><tt class="py-op">]</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">                        <tt class="py-name">Pau</tt> <tt class="py-op">=</tt> <tt class="py-name">eQhalf</tt><tt class="py-op">[</tt><tt class="py-name">aind</tt><tt class="py-op">,</tt><tt class="py-name">uind</tt><tt class="py-op">]</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">                        <tt class="py-name">Pax</tt> <tt class="py-op">=</tt> <tt class="py-name">eQhalf</tt><tt class="py-op">[</tt><tt class="py-name">aind</tt><tt class="py-op">,</tt><tt class="py-name">xind</tt><tt class="py-op">]</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">                        <tt class="py-name">PMuUu</tt> <tt class="py-op">+=</tt> <tt class="py-name">pia</tt> <tt class="py-op">*</tt> <tt class="py-name">Pau</tt><tt class="py-op">*</tt><tt class="py-name">Pau</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">                        <tt class="py-name">PMuUx</tt> <tt class="py-op">+=</tt> <tt class="py-name">pia</tt> <tt class="py-op">*</tt> <tt class="py-name">Pau</tt><tt class="py-op">*</tt><tt class="py-name">Pax</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">                    <tt class="py-comment"># This is 1-fux. For a given SNP with actual ancestral state</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">                    <tt class="py-comment"># u and derived allele x, this is 1 minus the probability</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">                    <tt class="py-comment"># that the outgroup will have u.</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">                    <tt class="py-comment"># Eqn 3 in HWB.</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">                    <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-op">-</tt> <tt class="py-name">PMuUu</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">PMuUu</tt> <tt class="py-op">+</tt> <tt class="py-name">PMuUx</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">                    <tt class="py-comment"># These aren't SNPs, so we can arbitrarily set them to 0</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">u</tt> <tt class="py-op">==</tt> <tt class="py-name">x</tt><tt class="py-op">:</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">                        <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">                     </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">                    <tt class="py-name">outlines</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">'%c%c%c %c %.6f'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">first</tt><tt class="py-op">,</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">third</tt><tt class="py-op">,</tt><tt class="py-name">u</tt><tt class="py-op">,</tt><tt class="py-name">res</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">linesep</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">outlines</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">newfile</tt><tt class="py-op">:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"> </tt>
<a name="zero_diag"></a><div id="zero_diag-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="zero_diag-toggle" onclick="return toggle('zero_diag');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#zero_diag">zero_diag</a><tt class="py-op">(</tt><tt class="py-param">Q</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="zero_diag-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="zero_diag-expanded"><a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">    Copy of Q altered such that diagonal entries are all 0.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">    <tt class="py-name">Q_nodiag</tt> <tt class="py-op">=</tt> <tt class="py-name">Q</tt><tt class="py-op">.</tt><tt class="py-name">copy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">Q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt class="py-name">Q_nodiag</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">Q_nodiag</tt> </tt>
</div><a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"> </tt>
<a name="tri_freq_dict_to_array"></a><div id="tri_freq_dict_to_array-def"><a name="L201"></a><tt class="py-lineno">201</tt> <a class="py-toggle" href="#" id="tri_freq_dict_to_array-toggle" onclick="return toggle('tri_freq_dict_to_array');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#tri_freq_dict_to_array">tri_freq_dict_to_array</a><tt class="py-op">(</tt><tt class="py-param">tri_freq_dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="tri_freq_dict_to_array-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="tri_freq_dict_to_array-expanded"><a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line"><tt class="py-docstring">    Convert dictionary of trinucleotide frequencies to array in correct order.</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">    <tt class="py-name">tripi</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-number">64</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">left</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-18', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">center</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-19', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt><tt class="py-op">,</tt><tt class="py-name">right</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="dadi.Misc.code" class="py-name" href="#" onclick="return doclink('link-20', 'code', 'link-0');">code</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">                <tt class="py-name">row</tt> <tt class="py-op">=</tt> <tt class="py-name">ii</tt><tt class="py-op">*</tt><tt class="py-number">16</tt> <tt class="py-op">+</tt> <tt class="py-name">jj</tt><tt class="py-op">*</tt><tt class="py-number">4</tt> <tt class="py-op">+</tt> <tt class="py-name">kk</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">                <tt class="py-name">tripi</tt><tt class="py-op">[</tt><tt class="py-name">row</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">tri_freq_dict</tt><tt class="py-op">[</tt><tt class="py-name">left</tt><tt class="py-op">+</tt><tt class="py-name">center</tt><tt class="py-op">+</tt><tt class="py-name">right</tt><tt class="py-op">]</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">tripi</tt> </tt>
</div><a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"> </tt>
<a name="total_instantaneous_rate"></a><div id="total_instantaneous_rate-def"><a name="L213"></a><tt class="py-lineno">213</tt> <a class="py-toggle" href="#" id="total_instantaneous_rate-toggle" onclick="return toggle('total_instantaneous_rate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#total_instantaneous_rate">total_instantaneous_rate</a><tt class="py-op">(</tt><tt class="py-param">Q</tt><tt class="py-op">,</tt> <tt class="py-param">pi</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="total_instantaneous_rate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="total_instantaneous_rate-expanded"><a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line"><tt class="py-docstring">    Total instantaneous substitution rate.</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">    <tt class="py-name">Qzero</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name" targets="Function dadi.Misc.zero_diag()=dadi.Misc-module.html#zero_diag"><a title="dadi.Misc.zero_diag" class="py-name" href="#" onclick="return doclink('link-21', 'zero_diag', 'link-21');">zero_diag</a></tt><tt class="py-op">(</tt><tt class="py-name">Q</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">dot</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.pi()=dadi.Spectrum_mod.Spectrum-class.html#pi"><a title="dadi.Spectrum_mod.Spectrum.pi" class="py-name" href="#" onclick="return doclink('link-22', 'pi', 'link-22');">pi</a></tt><tt class="py-op">,</tt> <tt class="py-name">Qzero</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"> </tt>
<a name="make_data_dict"></a><div id="make_data_dict-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="make_data_dict-toggle" onclick="return toggle('make_data_dict');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Misc-module.html#make_data_dict">make_data_dict</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="make_data_dict-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_data_dict-expanded"><a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"><tt class="py-docstring">    Parse SNP file and store info in a properly formatted dictionary.</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line"><tt class="py-docstring">    filename: Name of file to work with.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-docstring">    This is specific to the particular data format described on the wiki. </tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-docstring">    Modification for other formats should be straightforward.</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"><tt class="py-docstring">    The file can be zipped (extension .zip) or gzipped (extension .gz). If </tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"><tt class="py-docstring">    zipped, there must be only a single file in the zip archive.</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'.gz'</tt><tt class="py-op">:</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">gzip</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">gzip</tt><tt class="py-op">.</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'.zip'</tt><tt class="py-op">:</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">zipfile</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">        <tt class="py-name">archive</tt> <tt class="py-op">=</tt> <tt class="py-name">zipfile</tt><tt class="py-op">.</tt><tt class="py-name">ZipFile</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">        <tt class="py-name">namelist</tt> <tt class="py-op">=</tt> <tt class="py-name">archive</tt><tt class="py-op">.</tt><tt class="py-name">namelist</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">namelist</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Must be only a single data file in zip '</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">                             <tt class="py-string">'archive: %s'</tt> <tt class="py-op">%</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">archive</tt><tt class="py-op">.</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">namelist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">    <tt class="py-comment"># Skip to the header</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">        <tt class="py-name">header</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">header</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'#'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">            <tt class="py-keyword">break</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">    <tt class="py-name">allele2_index</tt> <tt class="py-op">=</tt> <tt class="py-name">header</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-string">'Allele2'</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">    <tt class="py-comment"># Pull out our pop ids</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">    <tt class="py-name">pops</tt> <tt class="py-op">=</tt> <tt class="py-name">header</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-name">allele2_index</tt><tt class="py-op">]</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">    <tt class="py-comment"># The empty data dictionary</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">    <tt class="py-name">data_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line"> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">    <tt class="py-comment"># Now walk down the file</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">SNP_ii</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'#'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">            <tt class="py-keyword">continue</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">        <tt class="py-comment"># Split the into fields by whitespace</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">        <tt class="py-name">spl</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">        <tt class="py-name">data_this_snp</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt class="py-comment"># We convert to upper case to avoid any issues with mixed case between</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">        <tt class="py-comment"># SNPs.</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt class="py-name">data_this_snp</tt><tt class="py-op">[</tt><tt class="py-string">'context'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">        <tt class="py-name">data_this_snp</tt><tt class="py-op">[</tt><tt class="py-string">'outgroup_context'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">        <tt class="py-name">data_this_snp</tt><tt class="py-op">[</tt><tt class="py-string">'outgroup_allele'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">        <tt class="py-name">data_this_snp</tt><tt class="py-op">[</tt><tt class="py-string">'segregating'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-name">allele2_index</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">        <tt class="py-name">calls_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">pop</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">pops</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">            <tt class="py-name">calls_dict</tt><tt class="py-op">[</tt><tt class="py-name">pop</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">+</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-name">allele2_index</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">+</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">        <tt class="py-name">data_this_snp</tt><tt class="py-op">[</tt><tt class="py-string">'calls'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">calls_dict</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">        <tt class="py-comment"># We name our SNPs using the final columns</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">        <tt class="py-name">snp_id</tt> <tt class="py-op">=</tt> <tt class="py-string">'_'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">spl</tt><tt class="py-op">[</tt><tt class="py-name">allele2_index</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">+</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pops</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">snp_id</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt><tt class="py-op">:</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">            <tt class="py-name">snp_id</tt> <tt class="py-op">=</tt> <tt class="py-string">'SNP_{0}'</tt><tt class="py-op">.</tt><tt class="py-name">format</tt><tt class="py-op">(</tt><tt class="py-name">SNP_ii</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">        <tt class="py-name">data_dict</tt><tt class="py-op">[</tt><tt class="py-name">snp_id</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">data_this_snp</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">data_dict</tt> </tt>
</div><a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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